MolNFT v1 · #23628 · protein + RNA

The structure of a ribosomal protein L1-mRNA complex

1U63 · 49 nt fragment of mRNA for L1: “The structure of a ribosomal protein L1-mRNA complex”. X-ray diffraction, 7 pockets (best druggability 0.76). MolNFT v1 #23628 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 1U63
Type: protein + RNA
Length: 526 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 49 nt fragment of mRNA for L1; 50S ribosomal protein L1P
UniProt: P54050
Pockets: 7 · best druggability 0.76

Structure

x-ray diffraction · 2 distinct chains · 37% helix, 19% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
B, D	49 nt fragment of mRNA for L1	rna	49	—	—
A, C	50S ribosomal protein L1P	protein	214	37% helix, 19% strand	P54050

Pockets

7 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	894	0.76	0.80	47	empty
2	496	0.74	0.83	39	empty
3	590	0.74	0.82	37	empty
4	533	0.73	0.81	52	empty
5	126	0.55	0.84	11	empty

Interfaces

6 interfaces between chains.

D–C · 1176 Å² buried · 31 hydrogen bonds · protein-nucleic
B–A · 1175 Å² buried · 28 hydrogen bonds · protein-nucleic
B–D · 467 Å² buried · 12 hydrogen bonds · nucleic-nucleic
D–A · 283 Å² buried · 4 hydrogen bonds · protein-nucleic
B–C · 262 Å² buried · 5 hydrogen bonds · protein-nucleic

Modifications

Observed in the structure: 12 modified (engineered).

Compared structures

1U63 · THE STRUCTURE OF A RIBOSOMAL PROTEIN L1-mRNA COMPLEX · the same entry in another collection · chain B against B, TM-score 1.00
P54050 · AlphaFold monomer V2.0 prediction for 50S ribosomal protein L1 (P54050) · a predicted model of the same protein · chain A against A, TM-score 0.93

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt P54050
Elsewhere: RCSB PDB 1U63 · PDBe 1U63 · UniProt P54050

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